exon.t

use lib 't';
use strict;

BEGIN { $| = 1;
	use Test ;
	plan tests => 27;
}

my $loaded = 0;
END {print "not ok 1\n" unless $loaded;}

use MultiTestDB;
use TestUtils qw(debug test_getter_setter count_rows);

our $verbose = 0; #set to 1 to turn on debug printouts

$loaded = 1;
my $multi = MultiTestDB->new();

ok(1);

my $db = $multi->get_DBAdaptor( 'core' );

ok($db);


# Exon specific tests

my $exonad = $db->get_ExonAdaptor();
my $slice_adaptor = $db->get_SliceAdaptor();

my $slice = $slice_adaptor->fetch_by_region('chromosome', '20',
                                            30_811_000,
                                            32_000_000);
ok($exonad);

my $exon = Bio::EnsEMBL::Exon->new();


$exon->start(1000);
ok(&test_getter_setter($exon, 'start', 200));

$exon->end(1400);
ok(&test_getter_setter($exon, 'end', 400));

$exon->strand(1);
ok(&test_getter_setter($exon, 'strand', -1));

$exon->phase(0);
ok(&test_getter_setter($exon, 'phase', -1));

$exon->slice( $slice );
ok(&test_getter_setter($exon, 'slice', $slice));

# should try to store (!)
$exon->end_phase( -1 );
ok(&test_getter_setter($exon, 'end_phase', 1));

#
# find supporting evidence for the exon
#
my @evidence = ();
my @fs = ();
push @fs, @{$db->get_DnaAlignFeatureAdaptor->fetch_all_by_Slice($slice)};
push @fs, @{$db->get_ProteinAlignFeatureAdaptor->fetch_all_by_Slice($slice)};

while(my $f = shift @fs) {
  #debug("feature at: " . $f->start . "-" . $f->end);
  next if $f->start > $exon->end || $f->end < $exon->start;
  push(@evidence, $f);